tbuckley/cabot-search huggingface dataset:
The Evaluation of Novel Targets for CAR T Therapy in Glioblastoma
Authors: Riza Alker, Peter Abel, David Griffiths, David Akhavan
Journal: Neuro-Oncology (2022)

Abstract AIMS The basis of this research revolves around the issue of limited expression of targetable tumour-specific antigens, heterogeneity, and mutation, which impede the development and success of CAR T therapy for glioblastoma. The research will identify an off-tumour cell target involved in tumour angiogenesis. The principal aim is to generate an off-tumour targeted CAR T and test their efficacy and safety in cell culture and animal models. METHOD Analyse the prevalence and distribution of the target molecules via immunohistochemistry (IHC). Confirm IHC results via mRNA extraction. Analyse the target molecule’s serum concentrations via the Luminex instrument. Generate the off-tumour targeted CAR T using lentivirus. Assess tumour burden and progression via a bioluminescent imaging system. Assess toxicity in vitro against human pericytes and in vivo by monitoring mouse weight and submitting histologic tissue for sectioning. RESULTS Utilise a scoring system to analyse the staining and correspond this to the serum concentrations to identify a blood-borne treatment response biomarker. If murine toxicity is observed, the CAR T construct will be affinity matured to selectively target molecules expressed at a cancerous level. A tandem bi-specific CAR T cells may also be created to mitigate immune escape and enhance anti-tumour efficacy. CONCLUSION The search for an off-tumour cell target for CAR T therapy in glioblastoma has not yet been completed. The discovery and validation of the novel molecule as a biomarker of treatment response would be a unique finding.
Cardiovascular Events After Primary Malignant and Non-Malignant Brain Tumour Diagnosis: A Population Matched Cohort Study in Wales (United Kingdom)
Authors: Michael T C Poon, Kai Jin, Paul Brennan, Jonine Figueroa, Cathie Sudlow
Journal: Neuro-Oncology (2022)

Abstract AIMS It is uncertain whether the elevated cardiovascular diseases (CVD) risks in patients with brain tumours is due to differences in the distribution of risk factors. We compared CVD risks among patients with a primary brain tumour to a matched general population cohort. METHOD Using data from the Secured Anonymised Information Linkage (SAIL) Databank in Wales, we identified adults aged ≥18 years with a diagnosis of brain tumour identified in the cancer registry between 2000-2014, and a matched cohort (case-to-control ratio 1:5) by age, sex and primary care provider from the general population. Outcomes included fatal and non-fatal major vascular events and venous thromboembolism (VTE). We used multivariable Cox models adjusted for clinical risk factors to compare risks. RESULTS There were 2,869 and 3,931 people diagnosed with malignant and non-malignant brain tumours, respectively, in Wales. They were matched to 33,785 controls. Within the first year of tumour diagnosis, malignant tumour was associated with VTE (hazard ratio [HR] 21.58, 95% confidence interval 16.12-28.88) and stroke (HR 3.32, 2.44-4.53). People with malignant tumour surviving one year had higher risks of VTE (HR 2.20, 1.52-3.18) and stroke (HR 1.45, 1.00-2.10) compared to their matched controls. Individuals with non-malignant tumours had higher risks of VTE (HR 3.72, 2.73-5.06), stroke (HR 4.06, 3.35-4.93) and aortic and peripheral arterial disease (HR 2.09, 1.26-3.48) within the first year of diagnosis compared with their controls. CONCLUSION The elevated risks of CVD suggest risk reduction a potential strategy to improve life quality and survival in people with malignant and non-malignant brain tumour.
Glioma Cell Invasion Is Dependent Upon the DNA Damage Response Kinase ATR
Authors: Joanna Birch, Karen Strathdee, Sarah Derby, Anna Koessinger, Anthony Chalmers, Jim Norman, Ross Carruthers
Journal: Neuro-Oncology (2022)

Abstract AIMS Gliomas have high levels of DNA replication stress and clinical trials of inhibitors of the key replication stress response protein ATR (ataxia telangiectasia and rad 3 related protein) as radiosensitisers are planned. We aimed to investigate the effect of ATR inhibition on the ability of glioma cells to infiltrate and invade the brain. METHOD Live cell imaging in a panel of primary glioma cultures following siRNA or pharmacological inhibition of ATR. Invasion following treatment of murine orthotopic gliomas was determined by immunohistochemistry. Intravital imaging of GFP expressing murine orthotopic xenografts via an intracranial window model of glioma was undertaken. RESULTS Invading margins of human glioma samples demonstrated increased pATR expression relative to core. Live cell imaging demonstrated reduced cell velocity following ATR inhibition (Berzosertib/BAY1895344) or siRNA. Cytoplasmic vacuolation occurred following ATRi or siRNA which were single walled structures which engulf high molecular weight dextran, compatible with blockade of macropinosome processing. Live cell imaging with GFP-integrin α5 and integrin recycling assays showed sequestration of integrins within macropinosomes and reduced integrin cycling. Intravital in vivo imaging of murine xenograft tumours confirmed vacuolation and dextran uptake following ATRi, whilst a further in vivo study demonstrated a reduction in invading tumour cells. CONCLUSION We demonstrate a novel role for ATR in facilitating macropinocytic vesicle trafficking and integrin recycling in GBM cells which results in a profound motility defect in vitro and in vivo. ATR inhibitors are entering early phase trials as radiation sensitisers and we propose that therapeutic benefit will extend beyond DNA damage potentiation.
CLIC1 and CLIC4 Ion Channel Deficiency Confers Increased Sensitivity to Tumour Treating Fields and Improved Survival in Paediatric Glioblastoma
Authors: Michaela Griffin, Surajit Basu, Raheela Khan, Stuart Smith
Journal: Neuro-Oncology (2022)

Abstract AIMS (1) To determine if specific and unique chloride intracellular channel (CLIC) expression patterns exist in paediatric glioblastoma. (2) To assess if these expression patterns can be exploited as a treatment strategy. (3) To assess the combination of ion channel manipulation with Tumour Treating Fields (TTFields). METHOD CLIC channel expression patterns were identified via multivariate analysis of in-house and publicly available data sets and RNA sequencing of in-house patient tumour samples. siRNA depletion or inhibition via IAA94 of CLIC1 and CLIC4 was assessed using cell cycle, clonogenic, migration and proliferation assays, alone and in combination with TTFields. Whole transcriptome gene expression analysis (Human Clairom™ Array) of pGBM cells treated with TTFields was carried out. RESULTS Clinical correlation determined that CLIC4 and CLIC1 deficiency was associated with increased overall survival, with siRNA depletion propagating a reduction in the proliferation, migration and invasion of pHGG cell lines associated with cell cycle arrest. Furthermore, CLIC1 and CLIC4 deficiency exacerbated the killing capacity of TTFields, reducing clonogenic and proliferative capabilities. Whole transcriptome gene expression analysis of paediatric GBM cell lines treated with TTFields and found that cells treated with TTfields exhibited a down-regulation in CLIC1 and CLIC4 compared to untreated cells. CONCLUSION These data provide rationale that genetic, electrical, and pharmacological manipulation of ion channels can reduce the capacity of childhood brain tumours to proliferate and invade. CLIC channels may be a suitable target for combination therapy to enhance the treatment efficacy of TTfields and help bring this non-invasive therapy to paediatric patients.
Computer-aided Design of Novel CDK5 Inhibitors; Towards New Treatments of Glioblastoma
Authors: Zahra Khan, Izabela Stasik, Joseph Hayes
Journal: Neuro-Oncology (2022)

Abstract AIMS Design and statistically optimize an in silico screening protocol; apply the screening protocol to a compound database; in vitro validation of selected inhibitors (isolated CDK5 enzyme binding assay). METHOD Two large compound databases, ZINC15 and Analyticon Discovery, were used to screen for potential CDK5 ATP-binding site inhibitors. They were first filtered using a generated pharmacophore model and then virtually screened using Glide SP docking with a solved CDK5-p25 structure (PDB: 3O0G). The selected candidates were validated using enzyme binding assays to determine their inhibitory activity on CDK5, as well as against a panel of kinases. RESULTS Over 17,000 compounds were screened during molecular docking studies and of these, ~11,600 compounds returned which are predicted to bind to CDK5. The top 10% of docked compounds were analysed and 30 candidates were selected for single concentration screening at 50 µM concentrations. The 9 most potent compounds were selected for IC50 determinations and revealed 6 compounds with IC50 &amp;lt;10 µM. The selected novel compounds were also screened against a panel of kinases (CDK2, CDK5, CDK9, GSK-3β) with varying selective profiles observed. CONCLUSION Low micromolar potent compounds have been identified through in silico screening and validated in using in vitro binding assays. One flavonoid compound in particular, cirsiliol (IC50 = 5.90 µM), displayed best selectivity towards CDK5, a challenge in kinase inhibitor design. The identified compounds will now pass to cellular studies to determine their effect on Glioblastoma cell lines.
The Changing Landscape of Diffuse Low Grade Glioma (DLGG) Management in the West of Scotland: A Single Centres 10-Year Experience
Authors: Elliot Tilling, Simon Lammy, Elsie Bridgman, Hannah Johnson, Alexandru Stan, Aaron Taylor, Athanasios Grivas
Journal: Neuro-Oncology (2022)

Abstract AIMS Management strategies for patients diagnosed with diffuse low grade glioma (DLGG) remain controversial. Current evidence favours resection over biopsy. This has resulted in more aggressive intervention. We examined management trends in the West of Scotland over a 10 year period. METHOD Patients diagnosed with DLGG between 2010 and 2019 were included and grouped according to time of diagnosis: 1) 2010-2012, 2) 2013-2016 and 3) 2017-2019. Clinical characteristics, management and overall survival (OS) were investigated and comparatively analysed. Survival between resection and biopsy groups was also analysed. RESULTS 84 patients were included (n=25 in Group 1, n=35 in Group 2 and n=24 in Group 3). Biopsy was less commonly performed in Group 2 (17%) and Group 3 (21%) compared to Group 1 (56%) p=0.014. The frequency of post-operative seizures: G1: n=3 (12%), G2: n=1 (2.9%), G3: n=2 (8.3%) (p=0.385) and focal neurological deficit: G1: n=4 (16%), G2: n=8 (22.9%), G3: n=6 (25) (p=0.718) and mean length of stay (LoS) in days: G1: 7.7, G2: 8.8, G3: 7.4 (p = 0.548) were similar across the groups. Survival analysis revealed no significant difference between groups: G1 52%, G2 69%, G3 75% (p=0.172). Patients managed by resection (n=58) versus biopsy (n = 26) observed improved survival (resection OS 70% compared to biopsy OS 39% (p= 0.005)). CONCLUSION Resection results in improved survival over biopsy. This has resulted in an institutional change over time. But no significant difference was observed in OS between different time periods.
Surgical and Oncological Score to Estimate the Survival Benefit of Resection and Chemoradiotherapy in Elderly (≥70 Years) Glioblastoma Patients: A Preliminary Analysis Authors
Authors: Mark Zorman, Philip Webb, Mickaela Nixon, Sanskrithi Sravanam, Susan Honeyman, Meera Nandhabalan, Vasileios Apostolopoulos, Richard Stacey, Claire Hobbs, Puneet Plaha
Journal: Neuro-Oncology (2022)

Abstract AIMS Elderly patients with glioblastoma are perceived to face a poor prognosis with perceptions surrounding older age and a relative lack of randomized data contributing. This study aimed to evaluate survival prognosticators in elderly glioblastoma patients to more accurately guide their treatment. METHOD The records of 169 elderly (≥70 years) patients with a new diagnosis of glioblastoma who had undergone neurosurgical intervention were retrospectively examined for patient sex, age, performance status, comorbidities, MGMT promoter methylation, surgical intervention and chemoradiation regime. The adjusted survival impact of these factors was determined using Cox proportional hazards model and used to devise a two-stage scoring system to estimate patient survival at the stage of surgical (Elderly Glioblastoma Surgical Score, EGSS) and oncological management (Elderly Glioblastoma Oncological Score, EGOS). RESULTS The median overall survival (mOS) of the cohort was 28.8 weeks. Gross-total and subtotal resection were associated with improved survival compared to biopsy alone (respective mOS 65.3 and 28.1 vs 15.7 weeks, p&amp;lt;0.001). Hypofractionated radiotherapy (40Gy in 15 fractions) with Temozolomide was non-inferior to the Stupp protocol, p=0.72. Exploratory subgroup analysis revealed a significant benefit of Temozolomide-based approaches in MGMT-methylated patients as well as a trend towards improved survival in MGMT-unmethylated patients. Our EGSS and EGOS scores successfully estimated survival in this retrospective cohort with 65% and 73% accuracy. CONCLUSION Where appropriate and safe, elderly glioblastoma patients may benefit from surgical resection and combined chemoradiotherapy with Temozolomide. The proposed EGSS and EGOS scores take into account important prognostic factors to help guide which patients should receive such treatment.
Modelling SHH-Medulloblastoma Using Cerebellar Organoids
Authors: Max van Essen, Peter Kilfeather, Sally Cowley, John Jacob, Esther Becker
Journal: Neuro-Oncology (2022)

Abstract AIMS Medulloblastoma (MB) comprises four main groups (SHH, WNT, group 3 and group 4), with distinct molecular, clinical and demographic features. These differences suggest opportunities for tailored and improved treatment. Despite its promise, translation into targeted therapy has been slow, limited by the lack of laboratory models that recapitulate patient tumours. Sporadic and inherited forms of SHH-MB are frequently due to mutations in the tumour suppressor gene PTCH1. Here, we aim to exploit human induced pluripotent stem cells (hiPSC) and CRISPR/Cas9 gene editing, to target PTCH1 in a clinically relevant context, thereby establishing an innovative model of MB. METHOD CRISPR/Cas9 mutation of PTCH1 in hiPSCs was followed by their differentiation into cerebellar organoids. Mutant organoids were studied for early consequences on cerebellar development and tumorigenesis. RESULTS PTCH1-mutation resulted in enhanced SHH-pathway activity in cerebellar organoids. Homozygous PTCH1-mutation prevented the formation of cerebellar progenitor cells, closely mimicking the effects of high SHH- signalling on neuronal progenitors in early embryonal development. Heterozygous PTCH1-mutant hiPSCs could be differentiated into cerebellar organoids, displayed increased growth rate and expressed oncogenes specific to SHH-MB, resembling preneoplasia and MB stem cells. CONCLUSION These results show that cerebellar organoids are a promising new model to study early oncogenic events in MB. Our model presents opportunities for the discovery of new targets which could benefit patients with a genetic predisposition to MB in particular. Refined knowledge of early drivers will be invaluable to guide drug selection and improve prospects for clinical translation.
Introducing “Cloudbuster” as 3D Analysis and Quantification Tool of Cellular Glioma Morphologies in 3D Microscopy
Authors: Arndt Rohwedder, Sabine Knipp, Filomena Esteves, Michael Hale, Darren Treanor, Anke Bruning-Richardson
Journal: Neuro-Oncology (2022)

Abstract AIMS A faithful representation of real tumour conditions in vivo such as a 3D glioma spheroid in a 3D experimental setting has become highly desirable for brain tumour research as it aids the study of tumour behaviour such as cell invasion and initiation of metastasis. However, data resulting from such studies need to be accurately analysed to correctly assess, for example, inhibitor effects on spheroid morphology and cell migration. To aid 3D data analysis we aimed to develop a reliable system for quantification of observed morphological changes such as number, morphology and size of invasive cells and spheroid extensions. METHOD We established a novel workflow that reconstructs a 3D entity from, for example, microtome sectioned glioma spheroids or confocal image z-stacks into pointclouds and subsequent comparison of basic readout parameters. The workflow requires little computational effort. Sliced image stacks are successfully scaled down towards a 1x1x1 ratio at threshold with subsequent edge detection and transformed into a pointcloud and analysed within minutes on a standard workstation /computer, e.g. shared graphics (4x 1.80 GHz CPU, 15 GB RAM). RESULTS We were able to validate the usefulness of this workflow using 3D data generated by various means including z-stacks from confocal microscopy and immunohistochemistry sectioning and demonstrate the possibility to accurately characterize inhibitor effects in depth. CONCLUSION We developed and validated ‘Cloudbuster’ as a 3D quantification tool to accurately assess structural changes detected in brain tumour cells after drug treatment, resulting in a versatile and adaptable 3D morphology analysis tool.
A Retrospective Review of the Management of Lung Cancer Patients Referred into the Regional Neuro-Oncology Pathway in Merseyside, United Kingdom
Authors: Jonathan Heseltine, Ana Corte, Oliver Kennedy, Harry Sharples, Andrew Brodbelt, Shaveta Mehta
Journal: Neuro-Oncology (2022)

Abstract AIMS Brain metastases (BMs) are common in lung cancer and carry adverse prognostic significance. Such occurrences should be reviewed through a regional specialist neuro-oncology MDT. Our aim is to highlight which aspects of the pathway could be contributing to delays in the treatment of lung cancer patients with BMs. METHOD All lung cancer patients discussed at the Neuro-Oncology MDT in 2020 were identified. Details of the patient journey through the pathway from diagnosis to death were obtained from the Orion System, regional PACS system, regional neuro-oncology MDT notes and electronic case notes from Clatterbridge. RESULTS Full datasets were available for 100 patients discussed at the Neuro-Oncology MDT. 49 of these were patients presenting with BMs and lung cancer synchronously. Only 5 out of 13 (38%) of synchronous patients recommended for SRS received this treatment. 7 of 13 patients received a suboptimal treatment (best supportive care or whole-brain radiotherapy). Length of time from neuro-oncology MDT discussion to receiving SRS in the synchronous cohort was 47 versus 20.3 days in the asynchronous group. A review of all 13 cases found that 4 of the 7 cases of CNS-specific deterioration were potentially preventable. Further analysis of these cases revealed common themes of lengthy delays in histological sampling (9), delayed referral or discussion in the appropriate MDT (8) and not jointly referring to neuro-oncology and respiratory oncology (7). CONCLUSION Lung cancer patients with synchronous BMs receive SRS after full staging and biopsy. There is potential evidence of suboptimal outcomes due to inflexible MDT systems and delays for histology.
A Retrospective Review of the Clinical Outcomes of Lung Cancer Patients Referred into the Regional Neuro-Oncology Pathway in 2020 in Merseyside, United Kingdom
Authors: Jonathan Heseltine, Ana Corte, Oliver Kennedy, Harry Sharples, Andrew Brodbelt, Shaveta Mehta
Journal: Neuro-Oncology (2022)

Abstract AIMS The aim of this project was to review the outcomes of patients referred via our regional neuro-oncology pathway who received neurosurgery, SRS, whole brain radiotherapy (WBRT), chemotherapy (SACT) or best supportive care (BSC). METHOD All lung cancer patients discussed at our Neuro-Oncology MDT in 2020 were identified. Patient characteristics and outcomes were obtained from the regional lung and neuro-oncology MDT notes and electronic case notes from Clatterbridge Cancer Centre. Overall survival (OS) was calculated from the date of diagnostic scan to death. The date of data cut-off was 15/10/2021. RESULTS Full datasets were available for 100 patients discussed at the Neuro-Oncology MDT. 65 were adenocarcinomas, 4 had ALK or EGFR mutations and 49 were synchronously presenting with brain metastases and lung cancer. At data cut-off 84 deaths had occurred. The median OS in days was calculated for surgery (207), SRS (360), surgery and cavity boost (298), SACT (249), WBRT (102) and BSC (60). A grouped comparison of SRS and surgery versus other interventions or best supportive care found a statistically significant advantage favouring SRS or surgery (Median OS 360 days, p=0.001). When comparing the synchronous versus asynchronous setting, the combined median OS of the neurosurgical, SRS or SACT cohorts was 276 versus 170 days but there was no difference in WBRT or BSC. CONCLUSION This real-world data details the number of lung cancer patients referred to and receiving neurosurgery or SRS via the Merseyside neuro-oncology MDT. This data supports pre-existing evidence that those who receive SRS or neurosurgery have a superior OS.
Long Term Quality of Life Outcomes Following Surgical Resection Alone for Benign Paediatric Intracranial Tumours
Authors: Siddhant Kumar, Abdurrahman Islim, Richard Moon, Christopher Millward, Dawn Hennigan, Ali Bakhsh, Antonia Thorpe, Mitchell Foster, Barry Pizer, Conor Mallucci, Michael Jenkinson
Journal: Neuro-Oncology (2022)

Abstract AIMS Survivors of paediatric intracranial malignancies are at increased risk of psychosocial, neuro-developmental and functional impairment, important measures of patients’ well-being. This study aimed to evaluate long-term quality of life outcomes (QOL) in patients with benign paediatric brain tumours treated curatively with surgical resection alone. METHOD Cross-sectional cohort study of benign paediatric intracranial tumours managed with surgery alone between 2000-2015. Validated QOL questionnaires were administered: SF-36, QLQ-BN20, QLQ-C30 and PedsQLTM. RESULTS Twenty-three patients participated (median age at surgery 13 years; range 1-18), twelve were male. The most common diagnosis was pilocytic astrocytoma (n=15). Median time from surgery to participation was 11 years (range 6-19). Fourteen patients achieved A-level qualifications and two obtained an undergraduate degree. Twelve patients were employed, eight were studying and three were unemployed or volunteering. Twelve patients were currently driving. QOL outcomes demonstrated significant limitation from social functioning (p=0.03) and cognitive functioning (p=0.023) compared to the general population norms. Patients also experienced increased loss of appetite (p=0.009) and symptoms of nausea and vomiting (p=0.031). Ten patients were under transitional teenager and young-adult (TYA) clinic follow-up. TYA patients achieved higher levels of education (p=0.014), were more likely to hold a driver’s license (p=0.041) and had improved physical functioning (p=0.005) compared to patients not transitioned through these services. CONCLUSION Childhood brain-tumour survivors are particularly vulnerable and at greater risk of developing psychological, neuro-cognitive, socialisation and physical development challenges. Early identification, comprehensive assessment and specialist TYA cancer healthcare input are vital to support these patients and improve their quality of life.